Fix JSS formatting requests

[seananderson]

Replication Material:

• [x] The file replication-code-pcod.R contains

# from remotes::install_github('seananderson/ggsidekick')
theme_sleek <- function(base_size = 11, base_family = "") {
...
}

but replication-code-timings still contains

ggsidekick::theme_sleek() +

requiring to install the package from GitHub.

• [x] The following note is obtained

2: `aes_string()` was deprecated in ggplot2 3.0.0.
Please use tidy evaluation ideoms with `aes()`

It would seem preferable to use code which avoids such notes for current versions of R packages.

Manuscript style comments:

• [x] Please only introduce an abbreviation within the abstract if it is needed again within the abstract. Otherwise, please introduce it within the body of the manuscript.

• [x] For the code layout in R publications, we typically distinguish input/output using Sinput/Soutput (or equivalently CodeInput/CodeOutput). Unless there are special reasons to format it differently, the input should use the text width (up to 76 or 77 characters) and be indented by two spaces, e.g.,

begin{Sinput}
R> example_model <- lm(response ~ variable1 + variable2 + variable3, 
+    weights = w, data = mydata)
\end{Sinput}

• [x] All captions should appear below the corresponding figure/table. The captions should be in sentence style and end with a period. No additional formatting (such as \emph, f or \it) should be used for the caption.

• [x] All table row/column headers should also be in sentence style. There should not be further footnote-style annotations in tables; these should all be placed in the caption.

• [x] As a reminder, please make sure that:

  • \proglang, \pkg and \code have been used for highlighting throughout the paper (including titles and references), except where explicitly escaped.

References:

• [x] Journal of the Royal Statistical Society B (not: Journal of the Royal Statistical Society, Series B) for Large Spatial Data Sets.” Journal of the Royal Statistical Society Series B for Large Spatial Data Sets.” Journal of the Royal Statistical Society Series B

• [x] Springer-Verlag (not: Springer) Diggle PJ, Ribeiro PJ (2007). Model-Based Geostatistics. Springer. ISBN 978-0-387-48536-2.

• [x] John Wiley & Sons (not: Wiley, John Wiley & Sons Inc.) Wiley

• [x] Please make sure that all software packages are \cite{}'d properly.

• [x] All references should be in title style.

My notes:

• [x] "The models were fit on a 2022 14 inch M1 MacBook Pro with an Apple M1 Pro 10-core CPU and 32 GB of RAM in R 4.2.2 and the default Matrix library"
• [x] bold, pkg, code in captions!?